Bioinformatics Associate II

Base pay range

$52.24/hr - $65.30/hr

This is a 6-month contract position based in South San Francisco, CA. The schedule is 1 day onsite required and 4 days remote.

• Develop, automate, and maintain robust pipelines for RNA‑seq, WGS/WES, scRNA‑seq, or other sequencing datasets.
• Optimize workflows for reproducibility, scalability, and performance across HPC or cloud environments.
• Perform advanced computational analyses including Variant calling, Differential gene expression, Transcriptomic and epigenomic analysis, Pathway/enrichment analysis, and Genomic annotation.
• Conduct QC for FASTQ, BAM/CRAM, VCF, and related formats.
• Write efficient, reproducible, and well‑documented code in Python or R.
• Build custom tools for data integration, transformation, and visualization.
• Implement, evaluate, and adapt existing bioinformatics tools and algorithms.
• Integrate open‑source resources to support project objectives.
• Work closely with wet‑lab scientists to interpret data, troubleshoot issues, and align computational analyses with experimental design.
• Communicate complex findings clearly to technical and non‑technical audiences.
• Diagnose pipeline failures, data issues, and computational inefficiencies.
• Ensure data integrity, workflow reproducibility, and methodological rigor.
• Prepare clear reports, visualizations, and presentations summarizing analysis outcomes.
• Maintain precise documentation of workflows, code, and datasets.
• Stay current with bioinformatics tools, NGS technologies, and computational methods.

• Master’s degree is required (Bioinformatics, Computational Biology, Genomics, Computer Science, or related quantitative field).
• 5–10 years of hands‑on experience working in bioinformatics or computational genomics.
• Demonstrated proficiency in Python or R.
• Extensive experience analyzing NGS datasets and implementing standard workflows.
• Proficiency with key tools, including STAR, BWA, Bowtie2, GATK, Samtools, bcftools, DESeq2, EdgeR, Seurat, and Scanpy.
• Experience with public genomic databases (NCBI, Ensembl, UCSC, GTEx, TCGA).
• Strong understanding of statistics, experimental design, and computational biology principles.
• Proficiency using Git/Git Hub for version control.
• Excellent communication, problem‑solving, and organizational skills.
• Experience with workflow management systems (Nextflow, Snakemake, WDL/Cromwell) preferred.
• Background in cloud computing (AWS, GCP, Azure) and containerization (Docker, Singularity) preferred.
• Previous work with HPC clusters preferred.
• Experience with specialized sequencing applications such as scRNA‑seq/ATAC‑seq, long‑read sequencing (Pac Bio, ONT), and epigenomics assays preferred.

• Medical insurance – PPO, HMO & HSA
• 401k plan
• Employee Assistance Program
• Long‑term disability
• Weekly payroll
• Online timecard approval

R&D Partners is an equal‑opportunity employer.